Migrate to Python 3 (3.9.0)

[janjoswig]

Hi everybody,

this PR wants to make the gmx2qmmm code compatible with the recent version of Python 3.9.0 alongside a few other changes.

A detailed description will follow, but here are the main changes:

• I reorganized the project structure, so that gmx2qmmm becomes a proper Python package (setup.py, requirements.txt). This has the following advantages:

  • The package can be installed (no $PYTHONPATH or custom script location handling)
  • We can get rid of the imp.load_source procedure (deprecated in Python3)
  • The code can be tested (e.g. using pytest)
  • The main executable can be called by "python -m gmx2qmmm.gmx2qmmm -flags" from anywhere (no path maintenance)

• Dots have been removed from script names (e.g. "xyz_zmat_g16RevA_02.py") to make them importable

• The deprecated compiler.ast.flatten has been replaced by gmx2qmmm._helper._flatten

• Some cosmetic changes to comply with PEP8 using Black reformatting

• .gitignore file to exclude unnecessary files from the repo

• Explicit module imports and calls (e.g. import numpy as np instead of from numpy import linalg as LA

• Replaced sort() by sorted()

• Parenthesis for print() calls

• ...

Planned changes:

• Replace subprocess.call by the recommended subprocess.run
• ...

No actual changes have been made to the code base, so everything should still work as before (needs to be validated).

[janjoswig]

The examples (sp/opt) pass successfully with these changes.

[yuap94]

Thx! I have created a new branch for your py3.9 version